Restructure bam-input pipeline in `dnascope-pangenome` #252

	name: CI
	on:
	push:
	pull_request:

	jobs:
	ci:
	strategy:
	fail-fast: true
	matrix:
	python-version: ["3.11", "3.14"]
	os: [ubuntu-22.04] #, macos-latest, windows-latest]
	runs-on: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v5
	- uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install --upgrade poetry
	- name: Test build
	run: \|
	poetry config virtualenvs.in-project true
	poetry install
	. .venv/bin/activate
	sentieon-cli -h
	formatting:
	strategy:
	fail-fast: true
	runs-on: ubuntu-22.04
	steps:
	- uses: actions/checkout@v5
	- uses: actions/setup-python@v5
	with:
	python-version: "3.14"
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install --upgrade poetry
	poetry install --with dev
	- name: Install the project dependencies
	run: poetry install
	- name: Run black formatter
	run: poetry run black --check --exclude '__pycache__\|scripts\|sentieon_cli/archive.py' --line-length 79 sentieon_cli
	- name: Run mypy
	run: poetry run mypy sentieon_cli --exclude scripts
	- name: Run flake8
	run: poetry run flake8 .
	- name: Run the automated tests
	run: poetry run pytest -v
	- name: Run doct tests
	run: poetry run pytest --doctest-modules

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